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group_manager.cc
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			/**
			* Copyright (©) 2013-2023 EPFL (Ecole Polytechnique Fédérale de Lausanne)
			* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
			*
			* This file is part of Akantu
			*
			* Akantu is free software: you can redistribute it and/or modify it under the
			* terms of the GNU Lesser General Public License as published by the Free
			* Software Foundation, either version 3 of the License, or (at your option) any
			* later version.
			*
			* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
			* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
			* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
			* details.
			*
			* You should have received a copy of the GNU Lesser General Public License
			* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
			*/

			/* -------------------------------------------------------------------------- */
			#include "group_manager.hh"
			#include "aka_csr.hh"
			#include "data_accessor.hh"
			#include "element_group.hh"
			#include "element_synchronizer.hh"
			#include "mesh.hh"
			#include "mesh_accessor.hh"
			#include "mesh_global_data_updater.hh"
			#include "mesh_iterators.hh"
			#include "mesh_utils.hh"
			#include "node_group.hh"
			#include "node_synchronizer.hh"
			#include "periodic_node_synchronizer.hh"
			/* -------------------------------------------------------------------------- */
			#include <algorithm>
			#include <iterator>
			#include <list>
			#include <numeric>
			#include <queue>
			#include <sstream>
			#include <utility>
			/* -------------------------------------------------------------------------- */

			namespace akantu {

			/* -------------------------------------------------------------------------- */
			GroupManager::GroupManager(Mesh & mesh, const ID & id) : id(id), mesh(mesh) {

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			GroupManager::~GroupManager() = default;

			/* -------------------------------------------------------------------------- */
			NodeGroup & GroupManager::createNodeGroup(const std::string & group_name,
			bool replace_group) {
			AKANTU_DEBUG_IN();

			auto it = node_groups.find(group_name);

			if (it != node_groups.end()) {
			if (replace_group) {
			it->second.reset();
			} else {
			AKANTU_EXCEPTION(
			"Trying to create a node group that already exists:" << group_name);
			}
			}

			std::stringstream sstr;
			sstr << this->id << ":" << group_name << "_node_group";

			auto && ptr = std::make_unique<NodeGroup>(group_name, mesh, sstr.str());

			auto & node_group = *ptr;

			// \todo insert_or_assign in c++17
			if (it != node_groups.end()) {
			it->second = std::move(ptr);
			} else {
			node_groups[group_name] = std::move(ptr);
			}

			AKANTU_DEBUG_OUT();

			return node_group;
			}

			/* -------------------------------------------------------------------------- */
			template <typename T>
			NodeGroup &
			GroupManager::createFilteredNodeGroup(const std::string & group_name,
			const NodeGroup & source_node_group,
			T & filter) {
			AKANTU_DEBUG_IN();

			NodeGroup & node_group = this->createNodeGroup(group_name);
			node_group.append(source_node_group);
			if (T::type == FilterFunctor::_node_filter_functor) {
			node_group.applyNodeFilter(filter);
			} else {
			AKANTU_ERROR("ElementFilter cannot be applied to NodeGroup yet."
			<< " Needs to be implemented.");
			}

			AKANTU_DEBUG_OUT();
			return node_group;
			}

			/* -------------------------------------------------------------------------- */
			ElementGroup & GroupManager::createElementGroup(const std::string & group_name,
			Int dimension,
			bool replace_group) {
			AKANTU_DEBUG_IN();

			auto it = element_groups.find(group_name);
			if (it != element_groups.end()) {
			if (replace_group) {
			it->second.reset();
			} else {
			AKANTU_EXCEPTION("Trying to create a element group that already exists:"
			<< group_name);
			}
			}

			auto & new_node_group = createNodeGroup(group_name + "_nodes", replace_group);

			auto && ptr = std::make_unique<ElementGroup>(
			group_name, mesh, new_node_group, dimension,
			this->id + ":" + group_name + "_element_group");

			auto & element_group = *ptr;

			if (it != element_groups.end()) {
			it->second = std::move(ptr);
			} else {
			element_groups[group_name] = std::move(ptr);
			}

			AKANTU_DEBUG_OUT();

			return element_group;
			}

			/* -------------------------------------------------------------------------- */
			void GroupManager::destroyElementGroup(const std::string & group_name,
			bool destroy_node_group) {
			AKANTU_DEBUG_IN();

			auto eit = element_groups.find(group_name);
			if (eit != element_groups.end()) {
			if (destroy_node_group) {
			destroyNodeGroup(eit->second->getNodeGroup().getName());
			}
			element_groups.erase(eit);
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void GroupManager::destroyNodeGroup(const std::string & group_name) {
			AKANTU_DEBUG_IN();

			auto nit = node_groups.find(group_name);
			if (nit != node_groups.end()) {
			node_groups.erase(nit);
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			ElementGroup & GroupManager::createElementGroup(const std::string & group_name,
			Int dimension,
			NodeGroup & node_group) {
			AKANTU_DEBUG_IN();

			if (element_groups.find(group_name) != element_groups.end()) {
			AKANTU_EXCEPTION(
			"Trying to create a element group that already exists:" << group_name);
			}

			auto && ptr =
			std::make_unique<ElementGroup>(group_name, mesh, node_group, dimension,
			id + ":" + group_name + "_element_group");

			auto & element_group = *ptr;
			element_groups[group_name] = std::move(ptr);

			AKANTU_DEBUG_OUT();

			return element_group;
			}

			/* -------------------------------------------------------------------------- */
			template <typename T>
			ElementGroup & GroupManager::createFilteredElementGroup(
			const std::string & group_name, Int dimension, const NodeGroup & node_group,
			T & filter) {
			AKANTU_DEBUG_IN();

			if (T::type == FilterFunctor::_node_filter_functor) {
			auto & filtered_node_group = this->createFilteredNodeGroup(
			group_name + "_nodes", node_group, filter);

			AKANTU_DEBUG_OUT();
			return this->createElementGroup(group_name, dimension, filtered_node_group);
			}
			if (T::type == FilterFunctor::_element_filter_functor) {
			AKANTU_ERROR(
			"Cannot handle an ElementFilter yet. Needs to be implemented.");
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			class ClusterSynchronizer : public DataAccessor<Element> {
			using DistantIDs = std::set<std::pair<Idx, Idx>>;

			public:
			ClusterSynchronizer(GroupManager & group_manager, Int element_dimension,
			std::string cluster_name_prefix,
			ElementTypeMapArray<Idx> & element_to_fragment,
			const ElementSynchronizer & element_synchronizer,
			Int nb_cluster)
			: group_manager(group_manager), element_dimension(element_dimension),
			cluster_name_prefix(std::move(cluster_name_prefix)),
			element_to_fragment(element_to_fragment),
			element_synchronizer(element_synchronizer), nb_cluster(nb_cluster) {}

			auto synchronize() {
			auto & comm = Communicator::getStaticCommunicator();
			auto rank = comm.whoAmI();
			auto nb_proc = comm.getNbProc();

			/// find starting index to renumber local clusters
			Array<Int> nb_cluster_per_proc(nb_proc);
			nb_cluster_per_proc(rank) = nb_cluster;
			comm.allGather(nb_cluster_per_proc);

			starting_index = std::accumulate(nb_cluster_per_proc.begin(),
			nb_cluster_per_proc.begin() + rank, 0);

			auto global_nb_fragment =
			std::accumulate(nb_cluster_per_proc.begin() + rank,
			nb_cluster_per_proc.end(), starting_index);

			/// create the local to distant cluster pairs with neighbors
			element_synchronizer.synchronizeOnce(*this,
			SynchronizationTag::_gm_clusters);

			/// count total number of pairs
			Array<Int> nb_pairs(nb_proc); // This is potentially a bug for more than
			// 2**31 pairs, but due to a all gatherv after
			// it must be int to match MPI interfaces
			nb_pairs(rank) = Int(distant_ids.size());
			comm.allGather(nb_pairs);

			auto total_nb_pairs = std::accumulate(nb_pairs.begin(), nb_pairs.end(), 0);

			/// generate pairs global array
			auto local_pair_index =
			std::accumulate(nb_pairs.begin(), nb_pairs.end() + rank, 0);

			Array<Int> total_pairs(total_nb_pairs, 2);

			for (const auto & ids : distant_ids) {
			total_pairs(local_pair_index, 0) = ids.first;
			total_pairs(local_pair_index, 1) = ids.second;
			++local_pair_index;
			}

			/// communicate pairs to all processors
			nb_pairs *= 2;
			comm.allGatherV(total_pairs, nb_pairs);

			/// renumber clusters

			/// generate fragment list
			std::vector<std::set<Int>> global_clusters;
			Int total_nb_cluster = 0;

			Array<bool> is_fragment_in_cluster(global_nb_fragment, 1, false);
			std::queue<Int> fragment_check_list;

			while (not total_pairs.empty()) {
			/// create a new cluster
			++total_nb_cluster;
			global_clusters.resize(total_nb_cluster);
			std::set<Int> & current_cluster = global_clusters[total_nb_cluster - 1];

			auto first_fragment = total_pairs(0, 0);
			auto second_fragment = total_pairs(0, 1);
			total_pairs.erase(0);

			fragment_check_list.push(first_fragment);
			fragment_check_list.push(second_fragment);

			while (!fragment_check_list.empty()) {
			auto current_fragment = fragment_check_list.front();
			auto * total_pairs_end = total_pairs.data() + total_pairs.size() * 2;
			auto * fragment_found =
			std::find(total_pairs.data(), total_pairs_end, current_fragment);

			if (fragment_found != total_pairs_end) {
			auto position = fragment_found - total_pairs.data();
			auto pair = position / 2;
			auto other_index = (position + 1) % 2;
			fragment_check_list.push(total_pairs(pair, other_index));
			total_pairs.erase(pair);
			} else {
			fragment_check_list.pop();
			current_cluster.insert(current_fragment);
			is_fragment_in_cluster(current_fragment) = true;
			}
			}
			}

			/// add to FragmentToCluster all local fragments
			for (auto c : arange(global_nb_fragment)) {
			if (!is_fragment_in_cluster(c)) {
			++total_nb_cluster;
			global_clusters.resize(total_nb_cluster);
			auto & current_cluster = global_clusters[total_nb_cluster - 1];

			current_cluster.insert(c);
			}
			}

			/// reorganize element groups to match global clusters
			for (auto c : arange(global_clusters.size())) {

			/// create new element group corresponding to current cluster
			auto & cluster = group_manager.createElementGroup(
			cluster_name_prefix + "_" + std::to_string(c), element_dimension,
			true);

			/// append to current element group all fragments that belong to
			/// the same cluster if they exist
			for (auto gc : global_clusters[c]) {
			Int local_index = gc - starting_index;

			if (local_index < 0 \|\| local_index >= Int(nb_cluster)) {
			continue;
			}

			auto id =
			"tmp_" + cluster_name_prefix + "_" + std::to_string(local_index);
			AKANTU_DEBUG_ASSERT(group_manager.elementGroupExists(id),
			"Temporary fragment \"" << id << "\" not found");

			cluster.append(group_manager.getElementGroup(id));
			group_manager.destroyElementGroup(id, true);
			}
			}

			return total_nb_cluster;
			}

			private:
			/// functions for parallel communications
			inline Int getNbData(const Array<Element> & elements,
			const SynchronizationTag & tag) const override {
			if (tag == SynchronizationTag::_gm_clusters) {
			return elements.size() * sizeof(UInt);
			}

			return 0;
			}

			inline void packData(CommunicationBuffer & buffer,
			const Array<Element> & elements,
			const SynchronizationTag & tag) const override {
			if (tag != SynchronizationTag::_gm_clusters) {
			return;
			}

			for (const auto & el : elements) {
			/// for each element pack its global cluster index
			buffer << element_to_fragment(el) + starting_index;
			}
			}

			inline void unpackData(CommunicationBuffer & buffer,
			const Array<Element> & elements,
			const SynchronizationTag & tag) override {
			if (tag != SynchronizationTag::_gm_clusters) {
			return;
			}

			for (const auto & el : elements) {
			Idx distant_cluster;
			buffer >> distant_cluster;

			auto local_cluster = element_to_fragment(el) + starting_index;

			distant_ids.insert(std::make_pair(local_cluster, distant_cluster));
			}
			} // namespace akantu

			private:
			GroupManager & group_manager;
			Int element_dimension{-1};
			std::string cluster_name_prefix;
			ElementTypeMapArray<Idx> & element_to_fragment;
			const ElementSynchronizer & element_synchronizer;

			Int nb_cluster{0};
			DistantIDs distant_ids;

			Idx starting_index{0};
			}; // namespace akantu

			/* -------------------------------------------------------------------------- */
			/// \todo this function doesn't work in 1D
			Int GroupManager::createBoundaryGroupFromGeometry() {
			auto spatial_dimension = mesh.getSpatialDimension();

			return createClusters(spatial_dimension - 1, "boundary");
			}

			/* -------------------------------------------------------------------------- */
			Int GroupManager::createClusters(
			Int element_dimension, Mesh & mesh_facets, std::string cluster_name_prefix,
			const GroupManager::ClusteringFilter & filter) {
			return createClusters(element_dimension, cluster_name_prefix, filter,
			mesh_facets);
			}

			/* -------------------------------------------------------------------------- */
			Int GroupManager::createClusters(
			Int element_dimension, std::string cluster_name_prefix,
			const GroupManager::ClusteringFilter & filter) {

			MeshAccessor mesh_accessor(mesh);
			auto mesh_facets = std::make_unique<Mesh>(mesh.getSpatialDimension(),
			mesh_accessor.getNodesSharedPtr(),
			"mesh_facets_for_clusters");

			mesh_facets->defineMeshParent(mesh);
			MeshUtils::buildAllFacets(mesh, *mesh_facets, element_dimension,
			element_dimension - 1);

			return createClusters(element_dimension, cluster_name_prefix, filter,
			*mesh_facets);
			}

			/* -------------------------------------------------------------------------- */
			//// \todo if needed element list construction can be optimized by
			//// templating the filter class
			Int GroupManager::createClusters(Int element_dimension,
			const std::string & cluster_name_prefix,
			const GroupManager::ClusteringFilter & filter,
			Mesh & mesh_facets) {
			AKANTU_DEBUG_IN();

			auto nb_proc = mesh.getCommunicator().getNbProc();
			std::string tmp_cluster_name_prefix = cluster_name_prefix;

			std::unique_ptr<ElementTypeMapArray<Idx>> element_to_fragment;

			if (nb_proc > 1 && mesh.isDistributed()) {
			element_to_fragment =
			std::make_unique<ElementTypeMapArray<Idx>>("element_to_fragment", id);

			element_to_fragment->initialize(
			mesh, _nb_component = 1, _spatial_dimension = element_dimension,
			_element_kind = _ek_not_defined, _with_nb_element = true);
			tmp_cluster_name_prefix = "tmp_" + tmp_cluster_name_prefix;
			}

			ElementTypeMapArray<bool> seen_elements("seen_elements", id);
			seen_elements.initialize(mesh, _spatial_dimension = element_dimension,
			_element_kind = _ek_not_defined,
			_with_nb_element = true, _default_value = false);

			for_each_element(
			mesh,
			[&filter, &seen_elements](auto && el) {
			seen_elements(el) = not filter(el);
			},
			_spatial_dimension = element_dimension);

			Int nb_cluster = 0;

			std::vector<std::string> created_groups;

			for (auto ghost_type : ghost_types) {
			Element uns_el;
			uns_el.ghost_type = ghost_type;
			for (auto type :
			mesh.elementTypes(_spatial_dimension = element_dimension,
			_ghost_type = ghost_type, _element_kind = _ek_not_defined)) {
			uns_el.type = type;
			auto & seen_elements_vec = seen_elements(uns_el.type, uns_el.ghost_type);

			for (Int e = 0; e < seen_elements_vec.size(); ++e) {
			// skip elements that have been already seen
			if (seen_elements_vec(e)) {
			continue;
			}

			// set current element
			uns_el.element = e;
			seen_elements_vec(e) = true;

			auto group_name =
			tmp_cluster_name_prefix + "_" + std::to_string(nb_cluster);

			created_groups.push_back(group_name);

			/// create a new cluster
			auto & cluster =
			createElementGroup(group_name, element_dimension, true);
			++nb_cluster;

			// point element are cluster by themself
			if (element_dimension == 0) {
			cluster.add(uns_el, true, false);
			continue;
			}

			std::queue<Element> element_to_add;
			element_to_add.push(uns_el);

			/// keep looping until current cluster is complete (no more
			/// connected elements)
			while (not element_to_add.empty()) {

			/// take first element and erase it in the queue
			auto el = element_to_add.front();
			element_to_add.pop();

			/// if parallel, store cluster index per element
			if (nb_proc > 1 && mesh.isDistributed()) {
			(*element_to_fragment)(el) = nb_cluster - 1;
			}

			/// add current element to the cluster
			cluster.add(el, true, false);

			const auto & element_to_facets =
			mesh_facets.getSubelementToElement().get(el);

			for (auto && facet : element_to_facets) {
			if (facet == ElementNull) {
			continue;
			}

			const auto & connected_elements =
			const_cast<const Mesh &>(mesh_facets)
			.getElementToSubelement(facet);

			for (const auto & check_el : connected_elements) {

			// check if this element has to be skipped
			if (check_el == ElementNull \|\| check_el == el) {
			continue;
			}

			auto & seen_elements_current = seen_elements(check_el);

			if (not seen_elements_current) {
			seen_elements_current = true;
			element_to_add.push(check_el);
			}
			}
			}
			}
			}
			}
			}

			for (auto && gid : created_groups) {
			this->getElementGroup(gid).getNodeGroup().optimize();
			}

			if (nb_proc > 1 && mesh.isDistributed()) {
			ClusterSynchronizer cluster_synchronizer(
			this, element_dimension, cluster_name_prefix, element_to_fragment,
			this->mesh.getElementSynchronizer(), nb_cluster);
			nb_cluster = cluster_synchronizer.synchronize();
			}

			if (mesh.isDistributed()) {
			this->synchronizeGroupNames();
			}

			AKANTU_DEBUG_OUT();
			return nb_cluster;
			}

			/* -------------------------------------------------------------------------- */
			template <typename T>
			void GroupManager::createGroupsFromMeshData(const std::string & dataset_name) {
			std::set<std::string> group_names;
			const auto & datas = mesh.getData<T>(dataset_name);

			std::map<std::string, Int> group_dim;

			for (auto ghost_type : ghost_types) {
			for (auto type : datas.elementTypes(_ghost_type = ghost_type)) {
			const auto & dataset = datas(type, ghost_type);
			auto nb_element = mesh.getNbElement(type, ghost_type);
			AKANTU_DEBUG_ASSERT(dataset.size() == nb_element,
			"Not the same number of elements ("
			<< type << ":" << ghost_type
			<< ") in the map from MeshData ("
			<< dataset.size() << ") " << dataset_name
			<< " and in the mesh (" << nb_element << ")!");
			for (Int e(0); e < nb_element; ++e) {
			std::stringstream sstr;
			sstr << dataset(e);
			std::string gname = sstr.str();
			group_names.insert(gname);

			auto it = group_dim.find(gname);
			if (it == group_dim.end()) {
			group_dim[gname] = mesh.getSpatialDimension(type);
			} else {
			it->second = std::max(it->second, mesh.getSpatialDimension(type));
			}
			}
			}
			}

			for (auto && name : group_names) {
			createElementGroup(name, group_dim[name]);
			}

			if (mesh.isDistributed()) {
			this->synchronizeGroupNames();
			}

			Element el;
			for (auto ghost_type : ghost_types) {
			el.ghost_type = ghost_type;
			for (auto type : datas.elementTypes(_ghost_type = ghost_type)) {
			el.type = type;
			const auto & dataset = datas(type, ghost_type);
			auto nb_element = mesh.getNbElement(type, ghost_type);
			AKANTU_DEBUG_ASSERT(dataset.size() == nb_element,
			"Not the same number of elements in the map from "
			"MeshData and in the mesh!");

			auto nb_nodes_per_element = mesh.getNbNodesPerElement(el.type);

			auto cit =
			mesh.getConnectivity(type, ghost_type).begin(nb_nodes_per_element);

			for (Int e(0); e < nb_element; ++e, ++cit) {
			el.element = e;
			std::stringstream sstr;
			sstr << dataset(e);
			auto & group = getElementGroup(sstr.str());
			group.add(el, false, false);

			const auto & connect = *cit;
			for (auto node : connect) {
			group.addNode(node, false);
			}
			}
			}
			}

			for (auto && name : group_names) {
			getElementGroup(name).optimize();
			}
			}

			template void GroupManager::createGroupsFromMeshData<std::string>(
			const std::string & dataset_name);
			template void
			GroupManager::createGroupsFromMeshData<UInt>(const std::string & dataset_name);

			/* -------------------------------------------------------------------------- */
			void GroupManager::createElementGroupFromNodeGroup(
			const std::string & name, const std::string & node_group_name,
			Int dimension) {
			NodeGroup & node_group = getNodeGroup(node_group_name);
			ElementGroup & group = createElementGroup(name, dimension, node_group);

			group.fillFromNodeGroup();
			}

			/* -------------------------------------------------------------------------- */
			void GroupManager::printself(std::ostream & stream, int indent) const {
			std::string space(indent, AKANTU_INDENT);

			stream << space << "GroupManager [" << std::endl;

			std::set<std::string> node_group_seen;
			for (auto & group : iterateElementGroups()) {
			group.printself(stream, indent + 1);
			node_group_seen.insert(group.getNodeGroup().getName());
			}

			for (auto & group : iterateNodeGroups()) {
			if (node_group_seen.find(group.getName()) == node_group_seen.end()) {
			group.printself(stream, indent + 1);
			}
			}

			stream << space << "]" << std::endl;
			}

			/* -------------------------------------------------------------------------- */
			Int GroupManager::getNbElementGroups(Int dimension) const {
			if (dimension == _all_dimensions) {
			return element_groups.size();
			}

			return std::count_if(element_groups.begin(), element_groups.end(),
			[dimension](auto && eg) {
			return eg.second->getDimension() == dimension;
			});
			}

			/* -------------------------------------------------------------------------- */
			void GroupManager::checkAndAddGroups(DynamicCommunicationBuffer & buffer) {
			AKANTU_DEBUG_IN();

			Int nb_node_group;
			buffer >> nb_node_group;
			AKANTU_DEBUG_INFO("Received " << nb_node_group << " node group names");

			for (Int ng = 0; ng < nb_node_group; ++ng) {
			std::string node_group_name;
			buffer >> node_group_name;

			if (node_groups.find(node_group_name) == node_groups.end()) {
			this->createNodeGroup(node_group_name);
			}

			AKANTU_DEBUG_INFO("Received node goup name: " << node_group_name);
			}

			Int nb_element_group;
			buffer >> nb_element_group;
			AKANTU_DEBUG_INFO("Received " << nb_element_group << " element group names");
			for (Int eg = 0; eg < nb_element_group; ++eg) {
			std::string element_group_name;
			buffer >> element_group_name;
			std::string node_group_name;
			buffer >> node_group_name;
			Int dim;
			buffer >> dim;

			AKANTU_DEBUG_INFO("Received element group name: "
			<< element_group_name << " corresponding to a "
			<< Int(dim) << "D group with node group "
			<< node_group_name);

			auto & node_group = *node_groups[node_group_name];

			if (element_groups.find(element_group_name) == element_groups.end()) {
			this->createElementGroup(element_group_name, dim, node_group);
			}
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void GroupManager::fillBufferWithGroupNames(
			DynamicCommunicationBuffer & comm_buffer) const {
			AKANTU_DEBUG_IN();

			// packing node group names;
			Int nb_groups = this->node_groups.size();
			comm_buffer << nb_groups;
			AKANTU_DEBUG_INFO("Sending " << nb_groups << " node group names");

			auto nnames_it = node_groups.begin();
			auto nnames_end = node_groups.end();
			for (; nnames_it != nnames_end; ++nnames_it) {
			std::string node_group_name = nnames_it->first;
			comm_buffer << node_group_name;
			AKANTU_DEBUG_INFO("Sending node goupe name: " << node_group_name);
			}

			// packing element group names with there associated node group name
			nb_groups = this->element_groups.size();
			comm_buffer << nb_groups;
			AKANTU_DEBUG_INFO("Sending " << nb_groups << " element group names");

			for (auto && pair : this->element_groups) {
			auto & element_group = *(pair.second);
			std::string element_group_name = pair.first;
			std::string node_group_name = element_group.getNodeGroup().getName();
			Int dim = element_group.getDimension();

			comm_buffer << element_group_name;
			comm_buffer << node_group_name;
			comm_buffer << dim;

			AKANTU_DEBUG_INFO("Sending element group name: "
			<< element_group_name << " corresponding to a "
			<< Int(dim) << "D group with the node group "
			<< node_group_name);
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void GroupManager::synchronizeGroupNames() {
			AKANTU_DEBUG_IN();

			const auto & comm = mesh.getCommunicator();
			auto nb_proc = comm.getNbProc();
			auto my_rank = comm.whoAmI();

			if (nb_proc == 1) {
			return;
			}

			if (my_rank == 0) {
			for (Int p = 1; p < nb_proc; ++p) {
			DynamicCommunicationBuffer recv_buffer;
			auto tag = Tag::genTag(p, 0, Tag::_element_group);
			comm.receive(recv_buffer, p, tag);
			AKANTU_DEBUG_INFO("Got " << printMemorySize<char>(recv_buffer.size())
			<< " from proc " << p << " " << tag);
			this->checkAndAddGroups(recv_buffer);
			}

			DynamicCommunicationBuffer comm_buffer;
			this->fillBufferWithGroupNames(comm_buffer);

			AKANTU_DEBUG_INFO("Initiating broadcast with "
			<< printMemorySize<char>(comm_buffer.size()));
			comm.broadcast(comm_buffer);

			} else {
			DynamicCommunicationBuffer comm_buffer;
			this->fillBufferWithGroupNames(comm_buffer);

			auto tag = Tag::genTag(my_rank, 0, Tag::_element_group);
			AKANTU_DEBUG_INFO("Sending " << printMemorySize<char>(comm_buffer.size())
			<< " to proc " << 0 << " " << tag);
			comm.send(comm_buffer, 0, tag);

			DynamicCommunicationBuffer recv_buffer;
			comm.broadcast(recv_buffer);
			AKANTU_DEBUG_INFO("Receiving broadcast with "
			<< printMemorySize<char>(recv_buffer.size()));

			this->checkAndAddGroups(recv_buffer);
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			const ElementGroup &
			GroupManager::getElementGroup(const std::string & name) const {
			auto it = element_groups.find(name);
			if (it == element_groups.end()) {
			AKANTU_EXCEPTION("There are no element groups named "
			<< name << " associated to the group manager: " << id);
			}

			return *(it->second);
			}

			/* -------------------------------------------------------------------------- */
			ElementGroup & GroupManager::getElementGroup(const std::string & name) {
			auto it = element_groups.find(name);
			if (it == element_groups.end()) {
			AKANTU_EXCEPTION("There are no element groups named "
			<< name << " associated to the group manager: " << id);
			}

			return *(it->second);
			}

			/* -------------------------------------------------------------------------- */
			const NodeGroup & GroupManager::getNodeGroup(const std::string & name) const {
			auto it = node_groups.find(name);
			if (it == node_groups.end()) {
			AKANTU_EXCEPTION("There are no node groups named "
			<< name << " associated to the group manager: " << id);
			}

			return *(it->second);
			}

			/* -------------------------------------------------------------------------- */
			NodeGroup & GroupManager::getNodeGroup(const std::string & name) {
			auto it = node_groups.find(name);
			if (it == node_groups.end()) {
			AKANTU_EXCEPTION("There are no node groups named "
			<< name << " associated to the group manager: " << id);
			}

			return *(it->second);
			}

			/* -------------------------------------------------------------------------- */
			template <typename GroupsType>
			void GroupManager::renameGroup(GroupsType & groups, const std::string & name,
			const std::string & new_name) {
			auto it = groups.find(name);
			if (it == groups.end()) {
			AKANTU_EXCEPTION("There are no group named "
			<< name << " associated to the group manager: " << id);
			}

			auto && group_ptr = std::move(it->second);

			group_ptr->name = new_name;

			groups.erase(it);
			groups[new_name] = std::move(group_ptr);
			}

			/* -------------------------------------------------------------------------- */
			void GroupManager::renameElementGroup(const std::string & name,
			const std::string & new_name) {
			renameGroup(element_groups, name, new_name);
			}

			/* -------------------------------------------------------------------------- */
			void GroupManager::renameNodeGroup(const std::string & name,
			const std::string & new_name) {
			renameGroup(node_groups, name, new_name);
			}

			/* -------------------------------------------------------------------------- */
			void GroupManager::copyElementGroup(const std::string & name,
			const std::string & new_name) {
			const auto & grp = getElementGroup(name);
			auto & new_grp = createElementGroup(new_name, grp.getDimension());

			new_grp.getElements().copy(grp.getElements());
			}

			/* -------------------------------------------------------------------------- */
			void GroupManager::copyNodeGroup(const std::string & name,
			const std::string & new_name) {
			const auto & grp = getNodeGroup(name);
			auto & new_grp = createNodeGroup(new_name);

			new_grp.getNodes().copy(grp.getNodes());
			}

			/* -------------------------------------------------------------------------- */
			void GroupManager::onNodesAdded(const Array<Idx> & new_nodes,
			const NewNodesEvent & event) {
			for (auto && group : make_values_adaptor(element_groups)) {
			group->onNodesAdded(new_nodes, event);
			}
			}
			/* -------------------------------------------------------------------------- */

			} // namespace akantu

rAKA/src/mesh/group_manager.cc160eaf086982features/35-implementat…

group_manager.ccView Options

rAKA/src/mesh/group_manager.cc
160eaf086982features/35-implementat…

group_manager.cc
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